crossing96/oncoscreening huggingface dataset:
Treatment and surveillance for non-muscle-invasive bladder cancer: a clinical practice guideline (2021 edition).	"Non-muscle invasive bladder cancer (NMIBC) is a major type of bladder cancer with a high incidence worldwide, resulting in a great disease burden. Treatment and surveillance are the most important part of NIMBC management. In 2018, we issued ""Treatment and surveillance for non-muscle-invasive bladder cancer in China: an evidence-based clinical practice guideline"". Since then, various studies on the treatment and surveillance of NMIBC have been published. There is a need to incorporate these materials and also to take into account the relatively limited medical resources in primary medical institutions in China. Developing a version of guideline which takes these two issues into account to promote the management of NMIBC is therefore indicated. We formed a working group of clinical experts and methodologists. Through questionnaire investigation of clinicians including primary medical institutions, 24 clinically concerned issues, involving transurethral resection of bladder tumor (TURBT), intravesical chemotherapy and intravesical immunotherapy of NMIBC, and follow-up and surveillance of the NMIBC patients, were determined for this guideline. Researches and recommendations on the management of NMIBC in databases, guideline development professional societies and monographs were referred to, and the European Association of Urology was used to assess the certainty of generated recommendations. Finally, we issued 29 statements, among which 22 were strong recommendations, and 7 were weak recommendations. These recommendations cover the topics of TURBT, postoperative chemotherapy after TURBT, Bacillus Calmette-Guérin (BCG) immunotherapy after TURBT, combination treatment of BCG and chemotherapy after TURBT, treatment of carcinoma in situ, radical cystectomy, treatment of NMIBC recurrence, and follow-up and surveillance. We hope these recommendations can help promote the treatment and surveillance of NMIBC in China, especially for the primary medical institutions."	bladder
Analysis of Cancer Survival Associated With Immune Checkpoint Inhibitors After Statistical Adjustment: A Systematic Review and Meta-analyses.	IMPORTANCE: Appropriate clinical decision-making relies on accurate data interpretation, which in turn relies on the use of suitable statistical models. Long tails and early crossover-2 features commonly observed in immune checkpoint inhibitor (ICI) survival curves-raise questions as to the suitability of Cox proportional hazards regression for ICI survival analysis. Cox proportional hazards-Taylor expansion adjustment for long-term survival data (Cox-TEL) adjustment may provide possible solutions in this setting. OBJECTIVE: To estimate overall survival and progression-free survival benefits of ICI therapy vs chemotherapy using Cox-TEL adjustment. DATA SOURCES: A PubMed search was performed for all cataloged publications through May 22, 2022. STUDY SELECTION: The search was restricted to randomized clinical trials with search terms for ICIs and lung cancer, melanoma, or urothelial carcinoma. The publications identified were further reviewed for inclusion. DATA EXTRACTION AND SYNTHESIS: Cox proportional hazards ratios (HRs) were transformed to Cox-TEL HRs for patients with short-term treatment response (ie, short-term survivor) (ST-HR) and difference in proportions for patients with long-term survival (LT-DP) by Cox-TEL. Meta-analyses were performed using a frequentist random-effects model. MAIN OUTCOMES AND MEASURES: Outcomes of interest were pooled overall survival (primary outcome) and progression-free survival (secondary outcome) HRs, ST-HRs, and LT-DPs. Subgroup analyses stratified by cancer type also were performed. RESULTS: A total of 1036 publications was identified. After 3 levels of review against inclusion criteria, 13 clinical trials (7 in non-small cell lung cancer, 3 in melanoma, and 3 in urothelial carcinoma) were selected for the meta-analysis. In the primary analysis, pooled findings were 0.75 (95% CI, 0.70-0.81) for HR, 0.86 (95% CI, 0.81-0.92) for ST-HR, and 0.08 (95% CI, 0.06-0.10) for LT-DP. In the secondary analysis, the pooled values for progression-free survival were 0.77 (95% CI, 0.64-0.91) for HR, 1.02 (95% CI, 0.84-1.24) for ST-HR, and 0.10 (95% CI, 0.06-0.14) for LT-DP. CONCLUSIONS AND RELEVANCE: This systematic review and meta-analysis of ICI clinical trial results noted consistently larger ST-HRs vs Cox HRs for ICI therapy, with an LT-DP of approximately 10%. These results suggest that Cox HRs may not provide a full picture of survival outcomes when the risk reduction from treatment is not constant, which may aid in the decision-making process of oncologists and patients.	bladder
Network Pharmacology Research and Dual-omic Analyses Reveal the Molecular Mechanism of Natural Product Nodosin Inhibiting Muscle-Invasive Bladder Cancer in Vitro and in Vivo.	Bladder cancer, specifically, muscle-invasive bladder cancer (MIBC), is among the most common malignant tumors. Patients with MIBC who cannot tolerate standard drugs require novel treatments. Targeting apoptosis may help treat cancer, which may be achieved with the use of some natural products. Nodosin, found in Isodon serra (Maxim.) Kudo (known as Xihuangcao), may inhibit bladder cancer cells. Transcriptomics and proteomics dual-omic analyses revealed the network pharmacological mechanism: (1) blocking the S phase by up-regulating RPA2, CLSPN, MDC1, PDCD2L, and E2F6 gene expressions, suppressing cancer cell proliferation; (2) inducing apoptosis and autophagy and restraining ferroptosis by up-regulating HMOX1, G0S2, SQSTM1, FTL, SLC7A11, and AIFM2 gene expressions; (3) preventing cancer cell migration by down-regulating NEXN, LIMA1, CFL2, PALLD, and ITGA3 gene expressions. In vivo, nodosin inhibited bladder cancer cell growth in a model of xenograft tumor in nude mice. This study is the first to report basic research findings on the network pharmacological mechanism of cytotoxicity of bladder cancer cells by nodosin, providing novel evidence for the application of nodosin in the field of oncology; however, other mechanisms may be involved in the effects of nodosin for further research. These findings provide a foundation for the development of novel MIBC drugs.	bladder
S-phase - an independent prognostic marker in upper tract urothelial carcinoma.	OBJECTIVES: To evaluate S-phase fraction as a predictor of invasiveness and cancer-specific survival in upper tract urothelial carcinoma (UTUC). PATIENTS AND METHODS: One hundred and fifteen patients having undergone radical nephroureterectomy were analysed with histology in radical nephroureterectomy specimens as reference test and S-phase fraction as index test. Ploidy and S-phase were determined using flow cytometry. Differences in S-phase fraction were calculated between stages, grades (WHO 1999 and 2004 classifications), ploidy and patients that died of UTUC and those who did not. Five- and 10-year-cancer-specific survivals were calculated. Areas under the ROC curve (AUCs) of S-phase fraction in relation to tumour stage and to death from UTUC were measured. Multiple Cox regression was performed. RESULTS: Independent prognostic markers of death from UTUC were S-phase fraction and stage. Correlation between S-phase fraction and risk of dying from UTUC was strong, with a 17% greater risk of death from UTUC with every 1% increase in S-phase fraction, hazard ratio = 1.17, 95% CI = 1.10-1.25, p < 0.001, Spearman's rho ρ = 0.65. AUCs for S-phase fraction as predictors of stage and death from UTUC were 0.8 (95% CI = 0.705-0.894) and 0.77 (95% CI = 0.67-0.87), respectively. Cancer-specific survival was statistically significantly different between stages, ploidy and WHO 1999 grades, but not between WHO 2004 grades. This was also reflected in S-phase fraction, which differed in LG-G1 compared with LG-G2 and in HG-G2 compared with HG-G3. CONCLUSION: S-phase fraction was a good test for predicting both invasiveness and cancer-specific survival. Using both WHO 1999 and 2004 classifications, rather than one system alone, had a higher predictive value of cancer-specific survival.	bladder
Impact of sex on outcomes after surgery for non-muscle-invasive and muscle-invasive bladder urothelial carcinoma: a systematic review and meta-analysis.	PURPOSE: To assess the prognostic value of sex for non-muscle-invasive/muscle-invasive bladder urothelial carcinoma (NMIBC/MIBC) treated with radical surgery. METHODS: The PubMed, Web of Science, and Scopus databases were searched in November 2021 according to the Preferred Reporting Items for Systematic Review and Meta-analysis statement. Studies were deemed eligible if they involved the comparison of the overall, cancer-specific, progression, and recurrence-free survival of patients with NMIBC/MIBC. Formal sex-stratified meta-analyses of these outcomes were performed. RESULTS: Thirty-one studies, which included 32,525 patients with NMIBC, and 63 studies, which included 85,132 patients with MIBC, were eligible for review and meta-analysis. Female sex was associated with worse cancer-specific survival (pooled hazard ratio [HR], 1.21; 95% confidence interval [CI], 1.11-1.31) and overall survival (pooled HR, 1.02; 95% CI, 1.00-1.05) in patients with MIBC. In contrast, however, sex was not associated with cancer-specific survival (pooled HR, 1.01; 95% CI, 0.70-1.46), progression-free survival (pooled HR, 1.04; 95% CI, 0.88-1.24), and recurrence-free survival (pooled HR, 1.06; 95% CI, 0.98-1.16) in patients with NMIBC. CONCLUSIONS: Sex is associated with an increased risk of worse survival outcomes in patients with MIBC but not in those with NMIBC. Given the genetic and social differences between sexes, sex may represent a key factor in the clinical decision-making process.	bladder
Targeting the FGFR Pathway in Urothelial Carcinoma: the Future Is Now.	As we come to better understand cancer genomics, we are increasingly shifting towards precision medicine. FGFR has been elucidated as one of the oncogenic driver pathways in urothelial carcinoma, leading to exciting targeted drug development. Although many agents are being investigated, erdafitinib is the only FGFR inhibitor currently approved by the FDA for treating platinum-refractory metastatic urothelial carcinoma harboring susceptible FGFR2/3 alterations, with seemingly higher response rates than second-line chemotherapy or immunotherapy. In this review, we summarize the clinical data supporting FGFR inhibition, ways to optimize its use in routine clinical practice including FGFR testing, dosing, and toxicity management. We also highlight ongoing efforts evaluating combination strategies and testing in earlier treatment settings to further expand this targeted therapeutic approach in urothelial carcinoma.	bladder
Clinical presentation of bacille Calmette-Guérin (BCG) infections after BCG instillation therapy.	OBJECTIVES: To investigate the timing of the clinical presentation of various types of bacille Calmette-Guérin (BCG) infections in a Finnish population of patients with bladder cancer treated with BCG instillation therapy. PATIENTS AND METHODS: We identified patients with a history of post-instillation BCG infection from 1996 to 2016 using the Finnish Cancer Registry and the Finnish National Infectious Diseases Registry. We categorised infections as systemic if the infection was found in the non-urogenital system and genitourinary (GU) if the infection affected the urogenital tract. We calculated the time interval between the last BCG instillation and the presentation of the infection. The infection was considered late if the time interval was ≥1 year. RESULTS: A total of 100 patients with BCG infection were identified during the study period. In all, 39 (39%) infections presented as systemic and 61 (61%) were in the GU tract. The majority of the systemic infections presented rapidly after the last instillation, while five (13%) presented after a latency of ≥1 year. The presentation of GU infections was more heterogeneous, with 12 (20%) presenting as late infections. CONCLUSION: This study confirms the concept of early and late infection types, especially among systemic infections. However, late infections appeared to be rarer than previously described. Urologists should be aware of the possibility of late BCG infection if patients develop symptoms even several years after the BCG regimen.	bladder
Cell-Level Spatio-Temporal Model for a Bacillus Calmette-Guérin-Based Immunotherapy Treatment Protocol of Superficial Bladder Cancer.	Bladder cancer is one of the most widespread types of cancer. Multiple treatments for non-invasive, superficial bladder cancer have been proposed over the last several decades with a weekly Bacillus Calmette-Guérin immunotherapy-based therapy protocol, which is considered the gold standard today. Nonetheless, due to the complexity of the interactions between the immune system, healthy cells, and cancer cells in the bladder's microenvironment, clinical outcomes vary significantly among patients. Mathematical models are shown to be effective in predicting the treatment outcome based on the patient's clinical condition at the beginning of the treatment. Even so, these models still have large errors for long-term treatments and patients that they do not fit. In this work, we utilize modern mathematical tools and propose a novel cell-level spatio-temporal mathematical model that takes into consideration the cell-cell and cell-environment interactions occurring in a realistic bladder's geometric configuration in order to reduce these errors. We implement the model using the agent-based simulation approach, showing the impacts of different cancer tumor sizes and locations at the beginning of the treatment on the clinical outcomes for today's gold-standard treatment protocol. In addition, we propose a genetic-algorithm-based approach to finding a successful and time-optimal treatment protocol for a given patient's initial condition. Our results show that the current standard treatment protocol can be modified to produce cancer-free equilibrium for deeper cancer cells in the urothelium if the cancer cells' spatial distribution is known, resulting in a greater success rate.	bladder
Routine urethroscopic surveillance is of limited value after radical cystectomy: a single centre retrospective cohort analysis.	PURPOSE: The incidence of urethral recurrence (UR) following radical cystectomy (RC) for transitional cell carcinoma (TCC) of the bladder varies between 1.5 and 6%. There is debate over the timing of urethrectomy for patients undergoing RC. We evaluated the requirement for a formal surveillance programme for UR in patients after RC. METHODS: We retrospectively reviewed the outcomes of patients who underwent RC between 2006 and 2019. Females, non-TCC cases and patients with neo-bladder diversions were excluded. Histological prostatic urethral involvement at the time of RC was deemed high risk for UR. Carcinoma in-situ, multifocal tumours and bladder neck involvement were deemed intermediate risk and the absence of the above features was considered low risk. RESULTS: 417 patients underwent RC, 300 cases remained after exclusion criteria were applied. 42 patients were high-risk for UR, 102 patients were intermediate risk and 156 were low risk. Of the 300, 24 urethrectomy cases were recorded. Six cases of UR occurred. Of these, 5 presented with symptoms and only 1 case was detected by surveillance. Only 1 low-risk patient developed UR, 7 years post RC. Using our risk stratification, UR rates for high, intermediate and low-risk cohorts were 25%, 10.5% and 0.8%, respectively. CONCLUSIONS: In our cohort, routine surveillance for all patients with annual urethroscopy was of limited value in detecting UR post RC. Staged Urethrectomy for high and intermediate-risk patients, and patient counselling in self-identification of recurrence symptoms for low-risk patients will improve the early detection of UR.	bladder
[Optimal surveillance intensity of cystoscopy in intermediate-risk non-muscle invasive bladder cancer].	OBJECTIVE: To determine the optimal cystoscopic frequency for intermediate-risk non-muscle invasive bladder cancer. METHODS: Patients with intermediate-risk non-muscle invasive bladder cancer, who underwent transurethral resection of bladder tumor in Peking University People's Hospital from January 2001 to October 2019, were retrospectively analyzed. Their clinical, pathological and follow-up data were collected. In postoperative 2-year period, the patients were underwent cystoscopy every 3 to 6 months. Depending on recurrence and progression of the patients, we hypothesized three strategies of surveillance intensity in the first 2 years after surgery: model 1: 3-month intervals, model 2: 6-month intervals, and model 3: 12-month intervals. The differences in the numbers and time of delayed detection of recurrence and progression were compared among the three models. RESULTS: A total of 185 patients were enrolled, including 144 males (77.8%) and 41 females (22.2%). The median age was 68 (59-76) years. There were 118 cases (63.8%) with single tumor and 67 cases (36.2%) with multiple tumor. Of the patients 179 (96.8%) had stage Ta and 6 (3.2%) had stage T1. There were 108 cases (58.4%) with high-grade disease and 77 cases (41.6%) with low-grade disease. During the follow-up period of the first 2 years, 52 patients (28.1%) had recurrence, 133 cases (71.9%) had no recurrence, 11 cases (5.9%) had progression and 174 cases (94.1%) had no progression. Compared with model 1, 29 (55.8%) delayed detection of recurrence in model 2 vs. 41 (78.8%) delayed detection of recurrence in model 3, and the difference was statistically significant (P=0.012). The median delayed time of detecting recurrence was 1.00 months in model 1, 1.99 months in model 2 and 4.19 months in model 3, respectively. There were statistically significant differences between mode 1 and model 3 (P=0.001), and between model 2 and model 3 (P=0.013). Compared with model 1, 5 (45.4%) delayed detection of progression in model 2 vs. 8 (72.7%) delayed detection of progression in model 3, and the difference was not statistically significant. The median delayed time of detecting progression was 1.00 month in model 1, 2.00 months in model 2 and 3.00 months in model 3, respectively. There was no statistically significant difference among them. CONCLUSION: Although providing slightly slower detection of tumor recurrence and progression, compared with 3-month intervals of cystoscopy, 6-month intervals do not result in serious adverse outcomes and reduce cost and pain of the patients, which is feasible in intermediate-risk non-muscle invasive bladder cancer.	bladder
Assessment of Tolerability, Response and Complications of Concurrent Chemoradiation With Capecitabine and Cisplatin in Muscle-Invasive Bladder Cancer; A Single Arm Study.	PURPOSE: To evaluate the feasibility, tolerance and efficacy of cisplatin+capecitabine as a proposed combination in concurrent chemoradiotherapy for patients with muscle-invasive bladder cancer (MIBC). METHODS: MIBC patients with stage T2-T4aN0M0 participated in this single-arm clinical trial. After maximal TURBT, 66Gy/33 daily fractions of radiation were administered with concurrent chemotherapy of cisplatin (35 mg/m(2)) and capecitabine (625 mg/m(2)). The primary endpoint was treatment tolerability, defined as receiving capecitabine+cisplatin combination for at least 5 weeks during radiation therapy. The secondary endpoints included complete response (CR) and acute toxicity rates. RESULTS: This study included 19 MIBC patients from 2018 to 2019. Eighteen patients (94.7%, 95%CI: 75.4-99.0) completed the planned treatment course. Only one patient (5.26%, 95%CI: 0.9-24.6) discontinued the treatment due to grade-3 GI toxicity. Among those who completed the treatment, CR was seen in 12 patients (66.7%, 95% CI = 44.4-88.9) with no grade ≥ 3 toxicities. The most common grade-2 side effects during therapy were renal complications (57.9%), and the only grade-2 complication after therapy was urinary-related (11.1%). The median follow-up was 31 months and the median overall survival (OS) was 31 months. The 2-year OS was 78% (95% CI 58.4-97.6), Cystectomy-free survival was 61% (95% CI: 37.5-84.5), and the median OS after recurrence was 13 months. Distant metastases were the first type of recurrence in most patients with a recurrence, which occurred in 7 (36.8%) patients. Median metastasis-free survival (MFS) was 30 months, and 2-year MFS was 66% (95% CI:45-87). CONCLUSION: The promising tolerability rate seen with concurrent cisplatin+capecitabine in this study was comparable to the available literature. Thus, this combination concurrently with radiation warrants further studies in the context of chemoradiotherapy of MIBC.	bladder
Intravesical Therapy Compared to Radical Cystectomy Among Patients With Non-Muscle Invasive Bladder Cancer Requiring Additional Treatment After Induction BCG.	BACKGROUND: Many patients with recurrent high-risk non-muscle invasive bladder cancer after intravesical bacillus calmette-guerin (BCG) face a difficult decision between radical cystectomy (RC) or salvage intravesical therapy (IVT). We sought to determine if there is a difference in overall survival RC and IVT after previous treatment with BCG. METHODS: We performed a retrospective cohort study of patients with Ta, T1, and Tis bladder cancer treated with induction BCG in the SEER-Medicare dataset from 2000 to 2015. We used a proportional hazards regression model to compare differences in survival between patients having RC and IVT. We adjusted for confounding using a propensity score and stratified our analysis according to timing of treatment and stage at diagnosis. RESULTS: We identified 3940 patients who received either IVT (79%) or RC (21%) following induction BCG. Among patients treated within 12 months of BCG, there was no significant difference in survival between RC and IVT (HR 0.92, 95% CI 0.81-1.04) and 17% of patients having early IVT ultimately required RC. Among patients treated at least 12 months after BCG, RC was associated with worse survival than IVT (HR 1.19, 95% CI 1.06-1.35) and 10% of patients having late IVT ultimately required RC. CONCLUSION: Among patients with bladder cancer who required additional treatments after induction BCG, we did not observe a difference in overall survival between IVT and RC within 12 months of starting BCG. While RC remains the gold-standard for high risk recurrent NMIBC after BCG, bladder preservation with IVT may be appropriate for well-selected patients.	bladder
Fast Lasso-type safe screening for Fine-Gray competing risks model with ultrahigh dimensional covariates.	The Fine-Gray proportional sub-distribution hazards (PSH) model is among the most popular regression model for competing risks time-to-event data. This article develops a fast safe feature elimination method, named PSH-SAFE, for fitting the penalized Fine-Gray PSH model with a Lasso (or adaptive Lasso) penalty. Our PSH-SAFE procedure is straightforward to implement, fast, and scales well to ultrahigh dimensional data. We also show that as a feature screening procedure, PSH-SAFE is safe in a sense that the eliminated features are guaranteed to be inactive features in the original Lasso (or adaptive Lasso) estimator for the penalized PSH model. We evaluate the performance of the PSH-SAFE procedure in terms of computational efficiency, screening efficiency and safety, run-time, and prediction accuracy on multiple simulated datasets and a real bladder cancer data. Our empirical results show that the PSH-SAFE procedure possesses desirable screening efficiency and safety properties and can offer substantially improved computational efficiency as well as similar or better prediction performance in comparison to their baseline competitors.	bladder